Package gov.nih.mipav.model.file

Class FilePARREC

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FilePARREC
public class FilePARREC extends FileBase
The class reads and writes PAR/REC files. A right handed coordinate system is used with the positive axis pointing (Anterior/Posterior)A->P, (Foot/Head)F->H, and (Right/Left)R->L. * Updated September 16, 2011 by Beth Tyrie // This explains the derivation of the dicom transformation matrix and origin from the PARREC parameters. // The axial PAR file is KKZ_130213_4_1.PAR // The first slice of the axial dicom file is 20131023203338769.MR.dcm // The sagittal PAR file is KKZ_130213_3_1.PAR // The first slice of the sagittal dicom file is 20131107105801812.MR.dcm. // The coronal PAR file is KKZ_130213_10_1.PAR // The first slice of the coronal dicom file is 20131107105805315.MR.dcm. // The angles are the same for the header volume parameters and for every slice int ori; final int axial = 1; final int sagittal = 2; final int coronal = 3; ori = coronal; double angulation_rl = 0.0; double angulation_ap = 0.0; double angulation_fh = 0.0; switch(ori) { case axial: angulation_rl = -8.700; angulation_ap = -4.865; angulation_fh = 3.364; break; case sagittal: angulation_rl = 0.305; angulation_ap = -4.280; angulation_fh = 4.083; break; case coronal: angulation_rl = 3.931; angulation_ap = -4.031; angulation_fh = 4.346; } double angX = 0.0; double angY = 0.0; double angZ = 0.0; switch(ori) { case axial: angX = angulation_rl; angY = angulation_ap; angZ = angulation_fh; break; case sagittal: angX = angulation_ap; angY = -angulation_fh; angZ = -angulation_rl; break; case coronal: angX = angulation_rl; angY = -angulation_fh; angZ = angulation_ap; } double Sx = Math.sin(angX * Math.PI/180.0); double Sy = Math.sin(angY * Math.PI/180.0); double Sz = Math.sin(angZ * Math.PI/180.0); double Cx = Math.cos(angX * Math.PI/180.0); double Cy = Math.cos(angY * Math.PI/180.0); double Cz = Math.cos(angZ * Math.PI/180.0); // EulerOrder = ORDER_XYZ; // This is the Transformation matrix shown in the dicom header // The dicom transformation matrix or image.getMatrix() is the transpose of the matrix given by getPatientOrientation(). // image.getMatrix() and getPatientOrientation() contain just the rotation component. double m00=Cy*Cz; double m01=-Cy*Sz; double m02=Sy; double m10=Cz*Sx*Sy+Cx*Sz; double m11=Cx*Cz-Sx*Sy*Sz; double m12=-Cy*Sx; double m20=-Cx*Cz*Sy+Sx*Sz; double m21=Cz*Sx+Cx*Sy*Sz; double m22=Cx*Cy; TransMatrix tr = new TransMatrix(4); switch (ori) { case axial: tr.M00 = (float)m00; tr.M01 = (float)m01; tr.M02 = (float)m02; tr.M03 = 0; tr.M10 = (float)m10; tr.M11 = (float)m11; tr.M12 = (float)m12; tr.M13 = 0; tr.M20 = (float)m20; tr.M21 = (float)m21; tr.M22 = (float)m22; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; break; case sagittal: tr.M00 = -(float)m20; tr.M01 = -(float)m21; tr.M02 = -(float)m22; tr.M03 = 0; tr.M10 = (float)m00; tr.M11 = (float)m01; tr.M12 = (float)m02; tr.M13 = 0; tr.M20 = -(float)m10; tr.M21 = -(float)m11; tr.M22 = -(float)m12; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; break; case coronal: tr.M00 = (float)m00; tr.M01 = (float)m01; tr.M02 = (float)m02; tr.M03 = 0; tr.M10 = (float)m20; tr.M11 = (float)m21; tr.M12 = (float)m22; tr.M13 = 0; tr.M20 = -(float)m10; tr.M21 = -(float)m11; tr.M22 = -(float)m12; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; } System.out.println("image transMatrix = " + tr); double resX = 0.0; double resY = 0.0; double resZ = 0.0; switch(ori) { case axial: resX = 0.859375; resY = 0.859375; resZ = 1.0; break; case sagittal: resX = 0.42857143; resY = 0.42857143; resZ = 5.0; break; case coronal: resX = 0.3515625; resY = 0.3515625; resZ = 3.3; } // The header volume offsets and the individual slice offsets are all different // The header volume offsets correspond to (xDim - 1)/2, (yDim - 1)/2, (zDim - 1)/2 // The slice offsets correspond to (xDim - 1)/2, (yDim - 1)/2, zSlice. double rl_offset_center = 0.0; double ap_offset_center = 0.0; double fh_offset_center = 0.0; switch(ori) { case axial: rl_offset_center = 6.655; ap_offset_center = 3.537; fh_offset_center = 22.171; break; case sagittal: rl_offset_center = 8.844; ap_offset_center = -3.225; fh_offset_center = -0.535; break; case coronal: rl_offset_center = 6.147; ap_offset_center = 16.846; fh_offset_center = 16.330; } double offsetX = 0.0; double offsetY = 0.0; double offsetZ = 0.0; switch(ori) { case axial: offsetX = rl_offset_center; offsetY = ap_offset_center; offsetZ = fh_offset_center; break; case sagittal: offsetX = ap_offset_center; offsetY = -fh_offset_center; offsetZ = -rl_offset_center; break; case coronal: offsetX = rl_offset_center; offsetY = -fh_offset_center; offsetZ = ap_offset_center; } double dimX = 0.0; double dimY = 0.0; double dimZ = 0.0; switch(ori) { case axial: dimX = 256; dimY = 256; dimZ = 140; break; case sagittal: dimX = 560; dimY = 560; dimZ = 31; case coronal: dimX = 512; dimY = 512; dimZ = 47; } double originX = offsetX - m00 * resX * (dimX-1)/2 - m01 * resY * (dimY-1)/2- m02 * resZ * (dimZ-1)/2; double originY = offsetY - m10 * resX * (dimX-1)/2 - m11 * resY * (dimY-1)/2 - m12 * resZ * (dimZ-1)/2; double originZ = offsetZ - m20 * resX * (dimX-1)/2 - m21 * resY * (dimY-1)/2 - m22 * resZ * (dimZ-1)/2; if (ori == sagittal) { originY = -originY; originZ = -originZ; } else if (ori == coronal) { originY = -originY; } // These are the origins shown for dicom slice 0 System.out.println("originX = " + originX); System.out.println("originY = " + originY); System.out.println("originZ = " + originZ);

  • Field Details

    • hdrEXTENSIONS

      public static final String[] hdrEXTENSIONS
      The extensions of ANALYZE file.

    • imgEXTENSIONS

      public static final String[] imgEXTENSIONS

    • fileDir

      private String fileDir
      File directory of the image.

    • fileInfo

      private FileInfoPARREC fileInfo
      Reference to the file info. for an Analyze header

    • fileName

      private String fileName
      File name of the image.

    • image

      private ModelImage image
      The image read in from the file.

    • dtiparams

      private DTIParameters dtiparams
      Object to save DWI paramters to

    • vox_offset

      private float vox_offset
      Voxel offset tag used to read in the image.

    • fileInfoArray

      private FileInfoPARREC[] fileInfoArray

    • outInfo

      private FileInfoPARREC outInfo
      file info

    • VolMap

      private HashMap<String,String> VolMap
      vol map

    • SliceMap

      private HashMap<String,Integer> SliceMap
      slice map

    • VolParameters

      private HashMap<String,String> VolParameters
      vol parameters

    • SliceParameters

      private Vector<String> SliceParameters
      slice parameters

    • Slices

      private Vector<String> Slices
      slices

    • version

      private String version
      version

    • patientName

      private String patientName

    • examName

      private String examName
      exam name

    • protocolName

      private String protocolName
      protocol name

    • patientPosition

      private String patientPosition
      patient position

    • foldover

      private String foldover

    • sliceOrientPos

      private int sliceOrientPos

    • bValuePos

      private int bValuePos
      bFactorIndex

    • gradPos

      private int gradPos
      bFactorIndex

    • echoNumberPos

      private int echoNumberPos

    • dynamicScanNumberPos

      private int dynamicScanNumberPos

    • cardiacPhaseNumberPos

      private int cardiacPhaseNumberPos

    • imageTypeMRPos

      private int imageTypeMRPos

    • scanningSequencePos

      private int scanningSequencePos

    • scanPercentagePos

      private int scanPercentagePos

    • windowCenterPos

      private int windowCenterPos

    • windowWidthPos

      private int windowWidthPos

    • imageAngulationPos

      private int imageAngulationPos

    • imageOffcentrePos

      private int imageOffcentrePos

    • fmriStatusIndicationPos

      private int fmriStatusIndicationPos

    • imageTypeEDESPos

      private int imageTypeEDESPos

    • echoTimePos

      private int echoTimePos

    • dynamicScanBeginTimePos

      private int dynamicScanBeginTimePos

    • triggerTimePos

      private int triggerTimePos

    • numberOfAveragesPos

      private int numberOfAveragesPos

    • flipAnglePos

      private int flipAnglePos

    • cardiacFrequencyPos

      private int cardiacFrequencyPos

    • minimumRRIntervalPos

      private int minimumRRIntervalPos

    • maximumRRIntervalPos

      private int maximumRRIntervalPos

    • turboFactorPos

      private int turboFactorPos

    • inversionDelayPos

      private int inversionDelayPos

    • diffusionBValueNumberPos

      private int diffusionBValueNumberPos

    • gradientOrientationNumberPos

      private int gradientOrientationNumberPos

    • contrastTypePos

      private int contrastTypePos

    • diffusionAnisotropyTypePos

      private int diffusionAnisotropyTypePos

    • labelTypePos

      private int labelTypePos

    • contrastBolusAgentPos

      private int contrastBolusAgentPos

    • contrastBolusRoutePos

      private int contrastBolusRoutePos

    • contrastBolusVolumePos

      private int contrastBolusVolumePos

    • contrastBolusStartTimePos

      private int contrastBolusStartTimePos

    • contrastBolusTotalDosePos

      private int contrastBolusTotalDosePos

    • contrastBolusIngredientPos

      private int contrastBolusIngredientPos

    • contrastBolusIngredientConcentrationPos

      private int contrastBolusIngredientConcentrationPos

    • sliceOrientIndex

      private int sliceOrientIndex

    • bValueIndex

      private int bValueIndex

    • gradIndex

      private int gradIndex

    • echoNumberIndex

      private int echoNumberIndex

    • dynamicScanNumberIndex

      private int dynamicScanNumberIndex

    • cardiacPhaseNumberIndex

      private int cardiacPhaseNumberIndex

    • imageTypeMRIndex

      private int imageTypeMRIndex

    • scanningSequenceIndex

      private int scanningSequenceIndex

    • scanPercentageIndex

      private int scanPercentageIndex

    • windowCenterIndex

      private int windowCenterIndex

    • windowWidthIndex

      private int windowWidthIndex

    • imageAngulationIndex

      private int imageAngulationIndex

    • imageOffcentreIndex

      private int imageOffcentreIndex

    • fmriStatusIndicationIndex

      private int fmriStatusIndicationIndex

    • imageTypeEDESIndex

      private int imageTypeEDESIndex

    • echoTimeIndex

      private int echoTimeIndex

    • dynamicScanBeginTimeIndex

      private int dynamicScanBeginTimeIndex

    • triggerTimeIndex

      private int triggerTimeIndex

    • numberOfAveragesIndex

      private int numberOfAveragesIndex

    • flipAngleIndex

      private int flipAngleIndex

    • cardiacFrequencyIndex

      private int cardiacFrequencyIndex

    • minimumRRIntervalIndex

      private int minimumRRIntervalIndex

    • maximumRRIntervalIndex

      private int maximumRRIntervalIndex

    • turboFactorIndex

      private int turboFactorIndex

    • inversionDelayIndex

      private int inversionDelayIndex

    • diffusionBValueNumberIndex

      private int diffusionBValueNumberIndex

    • gradientOrientationNumberIndex

      private int gradientOrientationNumberIndex

    • contrastTypeIndex

      private int contrastTypeIndex

    • diffusionAnisotropyTypeIndex

      private int diffusionAnisotropyTypeIndex

    • labelTypeIndex

      private int labelTypeIndex

    • contrastBolusAgentIndex

      private int contrastBolusAgentIndex

    • contrastBolusRouteIndex

      private int contrastBolusRouteIndex

    • contrastBolusVolumeIndex

      private int contrastBolusVolumeIndex

    • contrastBolusStartTimeIndex

      private int contrastBolusStartTimeIndex

    • contrastBolusTotalDoseIndex

      private int contrastBolusTotalDoseIndex

    • contrastBolusIngredientIndex

      private int contrastBolusIngredientIndex

    • contrastBolusIngredientConcentrationIndex

      private int contrastBolusIngredientConcentrationIndex

    • echoNumber

      private int[] echoNumber

    • dynamicScanNumber

      private int[] dynamicScanNumber

    • cardiacPhaseNumber

      private int[] cardiacPhaseNumber

    • imageTypeMR

      private int[] imageTypeMR

    • scanningSequence

      private int[] scanningSequence

    • scanPercentage

      private int[] scanPercentage

    • windowCenter

      private int[] windowCenter

    • windowWidth

      private int[] windowWidth

    • imageAngulation

      private float[][] imageAngulation

    • imageOffcentre

      private float[][] imageOffcentre

    • fmriStatusIndication

      private int[] fmriStatusIndication

    • imageTypeEDES

      private int[] imageTypeEDES

    • echoTime

      private float[] echoTime

    • dynamicScanBeginTime

      private float[] dynamicScanBeginTime

    • triggerTime

      private float[] triggerTime

    • numberOfAverages

      private int[] numberOfAverages

    • flipAngle

      private float[] flipAngle

    • cardiacFrequency

      private int[] cardiacFrequency

    • minimumRRInterval

      private int[] minimumRRInterval

    • maximumRRInterval

      private int[] maximumRRInterval

    • turboFactor

      private int[] turboFactor

    • inversionDelay

      private float[] inversionDelay

    • diffusionBFactor

      private float[] diffusionBFactor

    • diffusionBValueNumber

      private int[] diffusionBValueNumber

    • gradientOrientationNumber

      private int[] gradientOrientationNumber

    • contrastType

      private String[] contrastType

    • diffusionAnisotropyType

      private String[] diffusionAnisotropyType

    • diffusion

      private float[][] diffusion

    • labelType

      private int[] labelType

    • contrastBolusAgent

      private String[] contrastBolusAgent

    • contrastBolusRoute

      private float[] contrastBolusRoute

    • contrastBolusVolume

      private String[] contrastBolusVolume

    • contrastBolusStartTime

      private String[] contrastBolusStartTime

    • contrastBolusTotalDose

      private float[] contrastBolusTotalDose

    • contrastBolusIngredient

      private String[] contrastBolusIngredient

    • contrastBolusIngredientConcentration

      private float[] contrastBolusIngredientConcentration

    • counter

      private int counter
      counter

    • rescaleIntercept

      private float[] rescaleIntercept
      floating point value = raw value/scaleSlope + rescaleIntercept/(rescaleSlope*scaleSlope)

    • rescaleSlope

      private float[] rescaleSlope

    • scaleSlope

      private float[] scaleSlope

    • sameSliceScalings

      private boolean sameSliceScalings
      True if the 3 values are the same for all slices

    • originalDataType

      private int originalDataType

    • isSortedByVolumes

      private boolean isSortedByVolumes
      normal par/rec are sorted by volumes...sometime, they are not sorted like this...instead they are based on slices if that is true, then we need to change around the image dataarray to make it sorted by volumes

    • numSlices

      private int numSlices
      num slices per volume

    • numVolumes

      private int numVolumes
      num vols in 4d dataset

    • changeToUnsignedInts

      boolean changeToUnsignedInts

  • Constructor Details

    • FilePARREC

      public FilePARREC(String[] fileNames)
      Creates a new FileAnalyze object.
      Parameters:
      fileNames - DOCUMENT ME!

    • FilePARREC

      public FilePARREC(String fName, String fDir)
      Constructs new file object.
      Parameters:
      fName - File name.
      fDir - File directory.

    • FilePARREC

      public FilePARREC(String fileName, String fileDirectory, FileInfoPARREC[] fileInfoArray, boolean changeToUnsignedInts)
      Constructor used by FileIO to write an image
      Parameters:
      fileName -
      fileDirectory -
      changeToUnsignedInts -
      fileInfoPARREC - []

    • FilePARREC

      public FilePARREC(String fileName, String fileDirectory, FileInfoBase fileInfo)
      Constructor used by FileIO to write an image
      Parameters:
      fileName -
      fileDirectory -
      fileInfo -

  • Method Details

    • finalize

      public void finalize()
      Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
      Overrides:
      finalize in class FileBase

    • setImage

      public void setImage(ModelImage image)
      Parameters:
      image -

    • getCompleteFileNameList

      public static String[] getCompleteFileNameList(String absolutePath)
      Returns the complete list of file names according to given file name.
      Parameters:
      absolutePath - one file name of PARREC.
      Returns:
      the complete list of file names.

    • getHeaderFile

      public static String getHeaderFile(String[] fileNames)
      ======= Returns the header file.
      Parameters:
      fileNames - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getImageFiles

      public static String[] getImageFiles(String[] fileNames)
      Returns the image file list.
      Parameters:
      fileNames - DOCUMENT ME!
      Returns:
      the image file list.

    • isHeaderFile

      public static boolean isHeaderFile(String absolutePath)
      Return true if the file specified by absolutePath is header file of PARREC.
      Parameters:
      absolutePath - the file name including path information.
      Returns:
      true if the specified file is header file.

    • isImageFile

      public static boolean isImageFile(String absolutePath)
      Return true if the file specified by absolutePath is image file of PARREC.
      Parameters:
      absolutePath - the file name including path information.
      Returns:
      true if the specified file is image file.

    • createImage

      public ModelImage createImage() throws IOException, OutOfMemoryError
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!
      OutOfMemoryError - DOCUMENT ME!

    • updateTransformMatrix

      private void updateTransformMatrix(FileInfoPARREC fileInfo, ModelImage image)

    • ConvertToMIPAVConvention

      public static TransMatrix ConvertToMIPAVConvention(TransMatrix mat)
      Converts translation matrix to mipav specific format

    • makeTranslationMatrix

      public static TransMatrix makeTranslationMatrix(double[] translations)
      Makes rotation matrix based on image off-centres that were stored in header and converted to orientation-specific values.

    • makeRotationMatrix

      public static TransMatrix makeRotationMatrix(int[] size, double[] rotations)
      Makes rotation matrix based on image angulations that were stored in header and converted to orientation-specific values.

    • getFileInfo

      public FileInfoPARREC getFileInfo()
      Returns the FileInfoAnalyze read from the file.
      Returns:
      File info read from file, or null if it has not been read.

    • getHeaderFile

      public String getHeaderFile()
      invalid input: '<'invalid input: '<'invalid input: '<'invalid input: '<'invalid input: '<'invalid input: '<'invalid input: '<' .working Returns the header file.
      Returns:
      DOCUMENT ME!

    • getImageFiles

      public String[] getImageFiles()
      Returns the image file list.
      Returns:
      the image file list.

    • readHeader

      public boolean readHeader(String imageFileName, String fileDir) throws IOException
      Reads the analyze header and stores the information in fileInfo.
      Parameters:
      imageFileName - File name of image.
      fileDir - Directory.
      Returns:
      Flag to confirm a successful read.
      Throws:
      IOException - if there is an error reading the header
      See Also:

    • readImage

      public ModelImage readImage(boolean one) throws IOException, OutOfMemoryError
      Reads an PAR/REC image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.
      Parameters:
      one - flag indicating one image of a 3D dataset should be read in.
      Returns:
      The image.
      Throws:
      IOException - if there is an error reading the file
      OutOfMemoryError
      See Also:

    • readImage

      public void readImage(float[] buffer) throws IOException, OutOfMemoryError
      Reads in a PAR/REC image (first the header file, then the raw file)
      Parameters:
      buffer - Image buffer to store image data into.
      Throws:
      IOException - if there is an error reading the file
      OutOfMemoryError
      See Also:

    • writeImage

      public void writeImage(ModelImage image, FileWriteOptions options) throws IOException
      Writes a PAR/REC format image and header.
      Parameters:
      image - Image model of data to write.
      Throws:
      IOException - if there is an error writing the file
      See Also:

    • getOffset

      private int getOffset(FileInfoPARREC fileInfo)
      Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
      Parameters:
      fileInfo - File info.
      Returns:
      offset

    • updateStartLocations

      private void updateStartLocations(FileInfoBase[] fileInfo)
      Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
      Parameters:
      fileInfo - DOCUMENT ME!

    • updateUnitsOfMeasure

      private void updateUnitsOfMeasure(FileInfoPARREC fileInfo, ModelImage image)
      Updates the units of Measure in the file info based on the voxUnits from an Analyze Header.
      Parameters:
      fileInfo - -- an Analyze file Info that has already been read
      image - -- a ModelImage that the fileInfo needs to be attached to

    • getCompleteFileNameListDefault

      public String[] getCompleteFileNameListDefault(String absolutePath)
      Gets the header and image file names given a header or image file name
      Parameters:
      absolutePath - header or image filename
      Returns:
      array [0] headerfilename [1] imagefilename

    • writeHeader

      public void writeHeader(ModelImage writeImage, String headerFileName, int beginSlice, int endSlice, int beginTime, int endTime, boolean rescale) throws IOException
      Parameters:
      writeImage -
      headerFileName -
      beginSlice -
      endSlice -
      beginTime -
      endTime -
      rescale -
      Throws:
      IOException

    • buildParVolMap

      private HashMap<String,String> buildParVolMap()

    • buildParSliceMap

      private HashMap<String,Integer> buildParSliceMap()